It has just come to my attention that Accelrys has withdrawn its excellent free molecular viewing package ViewerLite and now only offers ViewerPro which retails at $299. I would be interested (a) to know the reaction of other users of this software to the news and (b) if there are any alternative freeware applications that offer the same or similar functionality particularly for viewing crystal lattices. David Roberts
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Dr David R. Roberts Senior Lecturer in Chemistry Chemistry Department The Open University Walton Hall Milton Keynes MK7 6AA United Kingdom
Tel +44 (0)1908 653219 Fax +44 (0) 1908 858327 e-mail d.r.roberts@open.ac.uk www http://www2.open.ac.uk/Chemistry/DRR.html <http://www2.open.ac.uk/Chemistry/DRR.html>
It has just come to my attention that Accelrys has withdrawn its excellent free molecular viewing package ViewerLite and now only offers ViewerPro which retails at $299. I would be interested (a) to know the reaction of other users of this software to the news and (b) if there are any alternative freeware applications that offer the same or similar functionality particularly for viewing crystal lattices. I am somewhat surprised the Lite version has gone; amongst the "embedded" uses was Scifinder Scholar, where it was used as a 3D model viewer (although its activation to work under such was shall we say less obvious; I had a lengthy exchange with CAS about this about two months ago to clarify this aspect). I say embedded because the need to use Viewer was apparently hardcoded into the SciFinder application. The use of 3D viewers on the Web has gotten "messy" to say the least. Thus if you are viewing in a Web page, Chime is still available, but to a certain extent this is semi-hard coded into the Web page by being invoked using the <embed > element, which presupposes that the Browser is enhanced with a plugin. That in turn presupposes that a plugin for your particular OS/browser combination is available. Those of us who use eg MacOS X will have noticed no native Chime (and it sounds as if there never will be one; to be fair there is a workaround, which is to use the Classic mode of OS X, and a classic browser such as Netscape 4). I believe that the Chem3D viewer plugin is also still available as an alternative to Chime, although unfortunately the two plugins do not share quite the identical set of attributes for the <embed> element that allow Chime and Chem3D to be used interchangeably; the author of the Web page would normally author for one or the other and you have to use the one they expected you to use. This by the way was one of the objections to the use of <embed> in XHTML, since no common schema for defining the allowable attributes of this element could in reality be specified. An alternative method was to deploy applets, and for this something like the excellent JMol (http://jmol.sourceforge.net) continues to improve (being at version 6. For a deployed example, see both their page and eg http://www.ch.ic.ac.uk/local/organic/tutorial/ir/ ) There are quite a few others; I did summarise a few months ago at http://www.ch.ic.ac.uk/rzepa/talks/author/ . Again applets suffer from the supposition that the author drives how you will view the resulting molecule in the browser. There was supposed to be a solution to all this mess via the <object> element, which can cascade down through a series of options available to the person viewing the web page (we wrote an article about this a couple of years ago http://www.ch.ic.ac.uk/rzepa/ijc/hierarchical/ ) but despite this solution having been drafted quite some time ago, few modern browsers actually implement it well enough to work reliably (the only one we found two years ago was the iCab browser for the Mac; we have not tested the recent crop again). The "ultra modern" solution is to create the appropriate viewing instructions "on the fly", either by querying a database directly, or by carrying the "chemistry" in its own markup/database (e.g. CML) and then transforming eg the molecule to an appropriate screen rendering, which could be Chime, or JMol, or VRML, or SVG etc etc etc. Our Chimeral project exemplified that approach; the excellent metalloprotein database at http://metallo.scripps.edu/current/raw.html shows how a (MySQL) database can be queried. I am sure there are many other exemplars. None of which of course answers David's original question about viewing crystal lattices. Other than Viewer, I believe Crystalmaker http://www.crystalmaker.co.uk/ is probably the best, but again I think that is commercial with no "Lite" version. -- Henry Rzepa. Imperial College, Chemistry Dept. +44 0778 626 8220 +44 020 7594 5804 (Fax) chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)
On Wednesday 21 May 2003 08:42, Rzepa, Henry wrote:
On Tuesday 20 May 2003 16:43, D.R.Roberts wrote:
It has just come to my attention that Accelrys has withdrawn its excellent free molecular viewing package ViewerLite and now only offers ViewerPro which retails at $299. I would be interested (a) to know the reaction of other users of this software to the news and (b) if there are any alternative freeware applications that offer the same or similar . functionality particularly for viewing crystal lattices.
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An alternative method was to deploy applets, and for this something like the excellent JMol (http://jmol.sourceforge.net) continues to improve (being at version 6. For a deployed example, see both their page and eg http://www.ch.ic.ac.uk/local/organic/tutorial/ir/ ) There are quite a few others; I did summarise a few months ago at http://www.ch.ic.ac.uk/rzepa/talks/author/ . Again applets suffer from the supposition that the author drives how you will view the resulting molecule in the browser.
<snip>
None of which of course answers David's original question about viewing crystal lattices. Other than Viewer, I believe Crystalmaker http://www.crystalmaker.co.uk/ is probably the best, but again I think that is commercial with no "Lite" version.
Jmol can display crystal lattices too nowadays. To see this in action, go this this page: http://jmol.sourceforge.net/scripting.html And click estron.cml link just below the second applet window. It will show you a hypothetical (but realistic) molecular crystal of the steroid. Note that Jmol broke up the molecules to put all atoms within the unit cell. (This is optional) kind regards, Egon Willighagen chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)
participants (3)
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                D.R.Roberts
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                E.L. Willighagen
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                Rzepa, Henry